As John Brennan moved into the CIA director’s office this month, another high-level transition was taking place down the hall.

A week earlier, a woman had been placed in charge of the CIA’s clandestine service for the first time in the agency’s history. She is a veteran officer with broad support inside the agency. But she also helped run the CIA’s detention and interrogation program after the Sept. 11, 2001, attacks and signed off on the 2005 decision to destroy videotapes of prisoners being subjected to treatment critics have called torture.

The woman, who remains undercover and cannot be named, was put in the top position on an acting basis when the previous chief retired last month. The question of whether to give her the job permanently poses an early quandary for Brennan, who is already struggling to distance the agency from the decade-old controversies.

Brennan endured a bruising confirmation battle in part over his own role as a senior CIA official when the agency began using water-boarding and other harsh interrogation methods. As director, he is faced with assembling the CIA’s response to a report by the Senate Intelligence Committee that documents ­abuses in the interrogation program and ­accuses the agency of misleading the White House and Congress over its effectiveness.

To help navigate the sensitive decision on the clandestine service chief, Brennan has taken the unusual step of assembling a group of three former CIA officials to evaluate the candidates. Brennan announced the move in a previously undisclosed notice sent to CIA employees last week, officials said.

“The director of the clandestine service has never been picked that way,” said a former senior U.S. intelligence official.

The move has led to speculation that Brennan is seeking political cover for a decision made more difficult by the re-emergence of the interrogation controversy and the acting chief’s ties to that program.

She “is highly experienced, smart and capable,” and giving her the job permanently “would be a home run from a diversity standpoint,” the former senior U.S. intelligence official said. “But she was also heavily involved in the interrogation program at the beginning and for the first couple of years.”

The former official, who spoke on the condition of anonymity in discussing internal agency matters, said that Brennan “is obviously hesitating” at making the chief permanent.

CIA officials disputed that characterization. “Given the importance of the position of the director of the National Clandestine Service, Director Brennan has asked a few highly respected former senior agency officers to review the candidates he’s considering for the job,” said Preston Golson, a CIA spokesman.

The group’s members were identified as former senior officials John McLaughlin, Stephen Kappes and Mary Margaret Graham.

Golson said Brennan will make the decision but added that “asking former senior agency officers to review the candidates will undoubtedly aid the selection process by making sure the director has the benefit of the additional perspectives from these highly experienced and respected intelligence officers.”

The service is the most storied part of the CIA. It sends spies overseas and carries out covert operations including running the agency’s ongoing drone campaign.

The service has also long been perceived as a male bastion that has blocked the career paths of women even while female officers have ascended to the top posts in other divisions, including the directors of analysis and science.

No woman has held the job of CIA director or led the clandestine service until now.

The acting chief, who according to public records is in her 50s, is part of a generation that over the past two decades has pushed through many obstacles confronting women. The CIA refused to comment on her background, but former colleagues said she mastered several languages and served multiple tours in Moscow and other cities overseas. She also held senior posts at CIA headquarters.

After the Sept. 11 attacks, she took on a senior assignment at the Counterterrorism Center, which put her in the chain of command on the interrogation and detention program, former officials said.

In a fateful decision, the CIA set up a video camera at its secret prison in Thailand shortly after it opened in the months after the attacks. The agency recorded more than 90 tapes of often-brutal interrogations, footage that became increasingly worrisome to officials as the legal basis for the program began to crumble.

When the head of the Counterterrorism Center, Jose Rodriguez, was promoted to head of the clandestine service in 2004, he took the female officer along as his chief of staff. According to former officials, the two repeatedly sought permission to have the tapes destroyed but were denied.

In 2005, instructions to get rid of the recordings went out anyway. Former officials said the order carried just two names: Rodriguez and his chief of staff.

The officer went on to hold top positions in London and New York before returning to Langley as deputy chief of the clandestine service. She became acting director on Feb. 28, when the previous head of the service, John Bennett, retired.

The Justice Department has twice investigated the tapes’ destruction and brought no charges against anyone at the CIA.

Former senior CIA officials said that outcome should clear any obstacles to the acting director getting the job permanently. But the seemingly dormant controversy over the interrogation program was revived by Brennan’s nomination and completion of a 6,000-page report from the Senate Intelligence Committee that accuses the agency of exaggerating the program’s results.

The acting director is mentioned in several passages of the report, according to officials familiar with its contents, although they declined to provide more details.

Amid calls for the public release of the report, Brennan faces having to devise a response that doesn’t alienate his workforce or the lawmakers who confirmed him for his job.

Former officials said the agency is planning an aggressive response. One said that an early draft response is “highly critical” of the findings and methodology of the study, pointing to “loads of holes” in the committee’s work.

Former senior CIA officials said creating a panel may help insulate Brennan from criticism regardless of his decision on the clandestine service job, enabling him to point to the guidance of agency veterans.

“But at the end of the day John is going to have to choose, even if his choice isn’t [the panel’s] number one choice,” a former senior CIA official said. “Some people’s demands for archaeology should not influence the director’s decision going forward on what’s best for the agency.”

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